Background: Atropine has is currently recommended to facilitate haemodynamic stability during critical care intubation. Our objective was to determine whether atropine use at induction influences ICU mortality. Methodology/Principal Findings: A 2-year prospective, observational study of all first non-planned intubations, September 2007–9 in PICU and Intensive Care Transport team of Hôpital Robert Debré, Paris, 4 other PICUs and 5 NICUs in the Paris Region, France. Follow-up was from intubation to ICU discharge. A propensity score was used to adjust for patient specific characteristics influencing atropine prescription. 264/333 (79%) intubations were included. The unadjusted ICU mortality was 7.2% (9/124) for those who received atropine compared to 15.7% (22/140) for those who did not (OR 0.42, 95%CI 0.19–0.95, p = 0.04). One child died during intubation (1/264, 0.4%). Two age sub-groups of neonates (≤28 days) and older children (>28 days, <8 years) were examined. This difference in mortality arose from the higher mortality in children aged over one month when atropine was not used (propensity score adjusted OR 0.22, 95%CI 0.06–0.85, p = 0.028). No effect was seen in neonates (propensity score adjusted OR 1.3, 95%CI 0.31–5.1 p = 0.74). Using the propensity score, atropine maintained the mean heart rate 45.9 bpm above that observed when no atropine was used in neonates (95%CI 34.3–57.5, p<0.001) and 43.5 bpm for older children (95%CI 25.5–61.5 bpm, p<0.001). Conclusions/Significance: Atropine use during induction was associated with a reduction in ICU mortality in children over one month. This effect is independent of atropine’s capacity to attenuate bradycardia during intubation which occurred similarly in neonates and older children. This result needs to be confirmed in a study using randomised methodology.